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Downloads and Upgrades Jul 1, 2011

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Strand Scientific Intelligence and Biobase have combined their respective products: Avadis NGS and Genome Trax.

By purchasing the integrated version of Genome Trax from Strand, Avadis NGS users will have access to Biobase's Transfac, which contains more than 3,000 regulatory sites; HGMD Professional, which includes 80,000 disease-linked mutations; over 600,000 ChIP-seq fragments; post-translational modifications; and transcription start sites.

In addition, license holders are given access to the Genome Trax online database, which holds additional information, including complete source citations.


Elsevier has added two new applications from Molecular Connections, a life science informatics company, to SciVerse Applications beta.

The first, Ask Extractor is based on Molecular Connections' XTractor, a platform for discovery, analysis, and modeling of biomedical information. The application provides search suggestions for life sciences terms entered into SciVerse Hub and SciVerse ScienceDirect. The second application, Journal Trends, enables users to discover top journals as a result of a given search query.


GenePattern 3.3.2 is now available.

This release includes the ability to upload files larger than 2 gigabytes, improved handling and visualization of uploaded files, and automatic launching and viewing of large data files with the Integrative Genomics Viewer.

Version 3.3.2 can be downloaded here and is also available for use on the GenePattern public server.


Gene Codes has released Sequencher 5.0.

The release incorporates new DNA sequence data alignment algorithms, such as Clustal, Maq, GSNAP, and Tablet, with SNP and methylation analysis for next-generation DNA sequence data analysis.


The Swiss Institute of Bioinformatics has launched an updated version of its web portal ExPASy, which provides a point of entry to more than 120 SIB bioinformatics resources in different areas including proteomics, genomics, phylogeny, systems biology, evolution, population genetics, and transcriptomics.

Among its capabilities is a new search feature that lets users query databases for content, and a visual guidance interface that lets users discover resources based on visual aids such as graphical images and tag clouds.


The Scan

CDC Calls Delta "Variant of Concern"

CNN reports the US Centers for Disease Control and Prevention now considers the Delta variant of SARS-CoV-2 to be a "variant of concern."

From FDA to Venture Capital

Former FDA Commissioner Stephen Hahn is taking a position at a venture capital firm, leading some ethicists to raise eyebrows, according to the Washington Post.

Consent Questions

Nature News writes that there are questions whether informed consent was obtained for some submissions to a database of Y-chromosome profiles.

Cell Studies on Multimodal Single-Cell Analysis, Coronaviruses in Bats, Urban Microbiomes

In Cell this week: approach to analyze multimodal single-cell genomic data, analysis of bat coronaviruses, and more.